Whole-scale metabolites were detected via mass spectrometer Xevo, G2-XS QTOF (Waters, UK) and identified based on the database KEGG. Software Progenesis QI (version 2.2) (Waters, UK) and R package metaX were used for statistical analysis of mass spectrometry data [54 (link)]. Variable Importance in the Projection (VIP) of the first two principal components in the multivariable PLS-DA model was used to screen differential metabolites by combining fold-change and q-value values. The VIP-score is a quantitative measure that indicates the strength and explanatory ability of each metabolite on the classification discrimination of samples in each group. Screening conditions are VIP≥1, fold-change ≥1.2 or ≤0.8333 and q-value<0.05. Metabolites satisfy the three conditions were identified as differential metabolites.
Progenesis qi version 2.2
Manufactured by Waters Corporation
Sourced in United Kingdom
Progenesis QI (version 2.2) is a software application developed by Waters Corporation for the analysis and interpretation of mass spectrometry data. It is designed to provide comprehensive, automated data processing and statistical analysis capabilities for untargeted metabolomics studies.
Automatically generated - may contain errors
8 protocols using progenesis qi version 2.2
1
Metabolomics Data Analysis Protocol
2
Metabolomics Analysis of Biological Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
An advanced Xevo G2-XS QTOF mass spectrometer (Waters, UK) was used for data acquisition, and the commercial software Progenesis QI (version 2.2) (Waters, UK) and the BGI metabolomics software package metaX [65 (link)] were used for mass spectrometry data analysis (filtering out ions with a relative standard deviation (RSD) greater than 30%). Identification was based on the Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ ) database. Significantly enriched pathways were assessed on the basis of the false discovery rate-adjusted hypergeometric test statistic (p ≤ 0.05). We used the prcomp function in the R software package to perform a PCA. The project uses variable importance in projection (VIP) values of the first two principal components in the multivariate PLS-DA model, combined with fold change (FC) and q-values from a univariate analysis to choose differentially expressed metabolites (DEMs) (VIP > 1 and FC > 1.2 or < 0.833 and with an adjusted q-value < 0.05 were considered significant). The cluster analysis used the pheatmap function in the pheatmap package in R.
3
Multivariate Analysis of Metabolomics Data
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A Xevo G2-XS QTOF (Waters, UK) system was used for MS data acquisition. Commercial software Progenesis QI version 2.2 (Waters, UK) and the independently developed metabolomics R package metaX (16 (link)) were used for MS data statistical analysis. Metabolite identification was performed using the HMDB (http://www.hmdb.ca/ ). The VIP (Variable Importance in Projection) values of the first two principal components of a multivariate partial least squares–discriminant analysis (PLS-DA) model were adopted, and the fold change and q values were combined to screen differentially expressed metabolites. The screening criteria were as follows: (1) VIP ≥ 1; (2) fold change ≥ 2 or ≤ 0.5; (3) P values < 0.01.
4
Plasma Lipid Profiling via QTOF-MS
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Lipids were extracted from individual plasma samples and then injected into the mass instrument in both positive and negative modes, with pooled extraction quality control (QC) samples at certain intervals. In this project, the advanced mass spectrometer Xevo G2-XS QTOF (Waters, UK) was used for mass spectrometry data collection, and the commercial software PROGENESIS QI (Version 2.2) (Waters, UK) and the independently developed metabonomics R software package metaX were used for statistical analysis of the mass spectrometry data, wherein metabolite identification was based on the databases HMDB and LipidMaps [17 (link)]. Univariate and multivariate analyses were conducted using R statistics software to identify and evaluate the significant metabolites among the groups.
5
Metabolite Profiling of HCMECs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
HCMECs with indicated treatment were harvested. After rinsed with PBS, the cells were incubated with 80% prechilled methanol for 30 minutes at -80°C. The supernatant was collected by centrifugation and dried by spin vacuum and dissolved in ACN solution. Then, 200 μL of sample was analyzed through an Thermo QE Plus LC-MS/MS system. Data were analyzed using the Progenesis QI (version 2.2) (Waters, UK) and R software suite (version 3.4.0). Univariate analysis and multivariate analysis were employed to screen the metabolites with differential expression.
6
Metabolomics Data Analysis Pipeline
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
An advanced Xevo G2-XS QTOF mass spectrometer (Waters, UK) was used for data acquisition, and commercial software Progenesis QI (version 2.2) (Waters, UK) and the BGI metabolomics software package metaX [62] were used for mass spectrometry data analysis (Filtering out ions with relative standard deviation (RSD) greater than 30%), while identification was based on the KEGG database. The project uses variable importance in projection (VIP) values of the first two principal components in the multivariate PLS-DA model, combined with fold change (FC) and q-values of univariate analysis to choose differentially expressed metabolites (DEMs) (VIP > 1 and FC >1.2 or < 0.833 and with an adjusted q-value < 0.05 were considered significant).
7
Plasma Lipid Profiling by QTOF-MS
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Lipids were extracted from individual plasma samples and then injected into the mass instrument in both positive and negative modes, with pooled extraction quality control (QC) samples at certain intervals. In this project, advanced mass spectrometer Xevo G2-XS QTOF (Waters, UK) is used for mass spectrometry data collection, and commercial software PROGENESIS QI (Version 2.2) (Waters, UK) and independently developed metabonomics R software package metaX are used for statistical analysis of mass spectrometry data, wherein metabolite identi cation is based on databases HMDB and LipidMaps [14] . Univariate and multivariate analyses were conducted using R statistics software to identify and evaluate the signi cant metabolites among the groups.
Metabolites extraction method 40 µL of each sample was added to the corresponding 96-well plate; 120 µL of pre-cooled isopropyl alcohol was added, shaken and mixed for 1 min, and then placed in a refrigerator at -20 ℃ for 2 h or overnight; centrifuged 4000 g at 4 ℃ for 30 min; Placed it in a new 96-well plate and diluted it with 225 µL of lipid complex solution (isopropanol: acetonitrile: water = 2: 1: 1); taked 20 µL of each sample and mixed it into QC sample; taked 60 µL of supernatant Transfer to a 96-well microtiter plate, sealed the label, and tested on the machine.
Metabolites extraction method 40 µL of each sample was added to the corresponding 96-well plate; 120 µL of pre-cooled isopropyl alcohol was added, shaken and mixed for 1 min, and then placed in a refrigerator at -20 ℃ for 2 h or overnight; centrifuged 4000 g at 4 ℃ for 30 min; Placed it in a new 96-well plate and diluted it with 225 µL of lipid complex solution (isopropanol: acetonitrile: water = 2: 1: 1); taked 20 µL of each sample and mixed it into QC sample; taked 60 µL of supernatant Transfer to a 96-well microtiter plate, sealed the label, and tested on the machine.
8
Plasma Lipid Profiling by QTOF-MS
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Lipids were extracted from individual plasma samples and then injected into the mass instrument in both positive and negative modes, with pooled extraction quality control (QC) samples at certain intervals. In this project, the advanced mass spectrometer Xevo G2-XS QTOF (Waters, UK) was used for mass spectrometry data collection, and the commercial software PROGENESIS QI (Version 2.2) (Waters, UK) and the independently developed metabonomics R software package metaX were used for statistical analysis of the mass spectrometry data, wherein metabolite identi cation was based on the databases HMDB and LipidMaps [15] . Univariate and multivariate analyses were conducted using R statistics software to identify and evaluate the signi cant metabolites among the groups [16] .
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!